#!/usr/bin/perl

##
## Copyright (C) 2008 Luciano Xumerle <luciano.xumerle@gmail.com>
##
## This program is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at your option) any later version.
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with this program.  If not, see <http://www.gnu.org/licenses/>.
##

use strict;
use warnings;

my $old   = '';
my $count = 0;

# if = -1 there is no limits
#my $MAX=10000;
my $MAX = -1;

my $ok = $MAX > 0;
foreach my $file (@ARGV)
{
    open( FILE, $file ) || die;
    while (<FILE>)
    {
        if ( $old ne '' && m/^[acgtn]+$/i )
        {
            print $old;
            print $_;
            $old = '';
            $count++;
        }
        else
        {
            if (m/^@/)
            {
                s/^@/>/;
                $old = $_;
            }
        }
        last if ( $ok && $count >= $MAX );
    }
    close FILE;
    last if ( $ok && $count >= $MAX );
}

